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| | ==CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND AN OXIDIZED PYRIMIDINE CONTAINING DNA AT 310K== | | ==CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND AN OXIDIZED PYRIMIDINE CONTAINING DNA AT 310K== |
| - | <StructureSection load='2xzu' size='340' side='right' caption='[[2xzu]], [[Resolution|resolution]] 1.82Å' scene=''> | + | <StructureSection load='2xzu' size='340' side='right'caption='[[2xzu]], [[Resolution|resolution]] 1.82Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2xzu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptococcus_hollandicus"_scholl_1891 "streptococcus hollandicus" scholl 1891]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XZU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2xzu]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_cremoris Lactococcus cremoris] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XZU FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.82Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=VET:[(1R,2S,4R)-2-HYDROXY-4-[(5R)-5-HYDROXY-5-METHYL-2,4-DIOXO-IMIDAZOLIDIN-1-YL]CYCLOPENTYL]METHYL+DIHYDROGEN+PHOSPHATE'>VET</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=VET:[(1R,2S,4R)-2-HYDROXY-4-[(5R)-5-HYDROXY-5-METHYL-2,4-DIOXO-IMIDAZOLIDIN-1-YL]CYCLOPENTYL]METHYL+DIHYDROGEN+PHOSPHATE'>VET</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1tdz|1tdz]], [[2xzf|2xzf]], [[1nnj|1nnj]], [[1pm5|1pm5]], [[1pji|1pji]], [[1xc8|1xc8]], [[1kfv|1kfv]], [[1pjj|1pjj]]</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2xzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xzu OCA], [https://pdbe.org/2xzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xzu RCSB], [https://www.ebi.ac.uk/pdbsum/2xzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xzu ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2xzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xzu OCA], [http://pdbe.org/2xzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xzu RCSB], [http://www.ebi.ac.uk/pdbsum/2xzu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xzu ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/FPG_LACLC FPG_LACLC]] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates.<ref>PMID:7704272</ref> | + | [https://www.uniprot.org/uniprot/FPG_LACLC FPG_LACLC] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates.<ref>PMID:7704272</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[DNA glycosylase|DNA glycosylase]] | + | *[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Streptococcus hollandicus scholl 1891]] | + | [[Category: Lactococcus cremoris]] |
| - | [[Category: Aller, P]] | + | [[Category: Large Structures]] |
| - | [[Category: Carrel, T]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Castaing, B]] | + | [[Category: Aller P]] |
| - | [[Category: Coste, F]] | + | [[Category: Carrel T]] |
| - | [[Category: Culard, F]] | + | [[Category: Castaing B]] |
| - | [[Category: Essalhi, K]] | + | [[Category: Coste F]] |
| - | [[Category: Gehrke, T H]] | + | [[Category: Culard F]] |
| - | [[Category: Izquierdo, M A]] | + | [[Category: Essalhi K]] |
| - | [[Category: Lebihan, Y V]] | + | [[Category: Gehrke TH]] |
| - | [[Category: Hydrolase-dna complex]]
| + | [[Category: Izquierdo MA]] |
| - | [[Category: Lyase]]
| + | [[Category: Lebihan YV]] |
| Structural highlights
Function
FPG_LACLC Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates.[1]
Publication Abstract from PubMed
DNA base-damage recognition in the base excision repair (BER) is a process operating on a wide variety of alkylated, oxidized and degraded bases. DNA glycosylases are the key enzymes which initiate the BER pathway by recognizing and excising the base damages guiding the damaged DNA through repair synthesis. We report here biochemical and structural evidence for the irreversible entrapment of DNA glycosylases by 5-hydroxy-5-methylhydantoin, an oxidized thymine lesion. The first crystal structure of a suicide complex between DNA glycosylase and unrepaired DNA has been solved. In this structure, the formamidopyrimidine-(Fapy) DNA glycosylase from Lactococcus lactis (LlFpg/LlMutM) is covalently bound to the hydantoin carbanucleoside-containing DNA. Coupling a structural approach by solving also the crystal structure of the non-covalent complex with site directed mutagenesis, this atypical suicide reaction mechanism was elucidated. It results from the nucleophilic attack of the catalytic N-terminal proline of LlFpg on the C5-carbon of the base moiety of the hydantoin lesion. The biological significance of this finding is discussed.
5-Hydroxy-5-methylhydantoin DNA lesion, a molecular trap for DNA glycosylases.,Le Bihan YV, Angeles Izquierdo M, Coste F, Aller P, Culard F, Gehrke TH, Essalhi K, Carell T, Castaing B Nucleic Acids Res. 2011 Aug;39(14):6277-90. Epub 2011 Apr 12. PMID:21486746[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Duwat P, de Oliveira R, Ehrlich SD, Boiteux S. Repair of oxidative DNA damage in gram-positive bacteria: the Lactococcus lactis Fpg protein. Microbiology. 1995 Feb;141 ( Pt 2):411-7. PMID:7704272
- ↑ Le Bihan YV, Angeles Izquierdo M, Coste F, Aller P, Culard F, Gehrke TH, Essalhi K, Carell T, Castaing B. 5-Hydroxy-5-methylhydantoin DNA lesion, a molecular trap for DNA glycosylases. Nucleic Acids Res. 2011 Aug;39(14):6277-90. Epub 2011 Apr 12. PMID:21486746 doi:10.1093/nar/gkr215
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